Question: Error with htseq-count
gravatar for bran.a.l.john
15 months ago by
bran.a.l.john10 wrote:

When I run htseq-count in galaxy I keep getting errors. The line in the history will look as follows:

##: htseq-count on data # and data # error An error occured with this dataset: Fatal error: Unknown error occured 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 500000 GFF lines processed. 600000 GFF lines processed. 700000 GFF lines processed. 800000 GFF lines proces

I have no idea how to fix this. I previously used HISAT2 to align my RNA-seq data and I am using a GFF file named "Homo_sapiens_UCSC_hg38.tar" that I downloaded from illumina. Does anyone know how to troubleshoot this issue?

ADD COMMENTlink modified 11 months ago by Jennifer Hillman Jackson25k • written 15 months ago by bran.a.l.john10

Did you solve that issue?


ADD REPLYlink written 13 months ago by n.goue50

I'm with the same issue using a gff file from NCBI

ADD REPLYlink written 11 months ago by rafaelccosta30
gravatar for Jennifer Hillman Jackson
11 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Errors with this tool can come up when the inputs are problematic.

  • First, use a GTF annotation dataset with this tool (GFF or GFF3 are not accepted input formats).
  • Next, regardless of the source, double check that the format is correct: Common datatypes explained
  • And finally, confirm that GTF is a match for the reference genome used for the mapping step (the input BAM datasets): Mismatched Chromosome identifiers

Prior Q&A in the right sidebar >>> cover the above and related solutions for this tool in the context of other examples. You can also review our FAQs and Tutorials for more usage help:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 11 months ago by Jennifer Hillman Jackson25k
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